This study involves a heterojunction (denoted as PPMS) with an intimate heterointerface and S-scheme architecture, which consisted of a conjugated polymer of protonated PyDTDO-3 featuring a donor-acceptor (D-A) configuration and a 2D-layered MoS2. The optimal PPMS-0.5% heterojunction exhibits a remarkable efficiency of 75.4 mmol g−1 h−1 in generating H2 when subjected to visible light illumination, representing an approximately 4.6 times enhancement compared to pure PyDTDO-3. To elucidate the photocatalytic mechanism, a range of characterization methods were utilized and calculations using density functional theory were carried out. The disparity in the work function between PyDTDO-3 and MoS2 results in the creation of a Fermi-level gap. Consequently, the establishment of a built-in electric field facilitates the occurrence of the electrons in MoS2 spontaneously transferring to PyDTDO-3 at the interface. The consumption of hole on the valence band of MoS2 is accelerated by the electron transfer from the lowest unoccupied molecular orbital (LUMO) of PyDTDO-3, according to a kinetic study using femtosecond transient absorption spectra (fs-TAS). Moreover, the S-scheme PPMS exhibits a lower Gibbs free energy (ΔGH*, 0.77 eV) in comparison to the individual component, indicating it facilitates the formation of the transitional state (H*) and the effective desorption of molecular hydrogen on PPMS. Both the promoting directed charge migration and the increasing active sites contribute to the boosted photocatalytic H2 evolution.